Translating pharmacogenetics Treat everyone as an individual
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Transcript of Translating pharmacogenetics Treat everyone as an individual
Translating pharmacogenetics Treat everyone as an individual DMET™ Plus Solution
Understanding the common variation in genes encoding for drug metabolism enzymes and drug transporters has the potential
to significantly impact clinical research by predicting the impact of an individual’s genetic variation on metabolic capacity. This
understanding takes us one step closer towards the vision of personalized medicine by helping to avoid adverse drug responses,
increasing treatment efficacy and providing both improved healthcare outcomes as well as substantial economic benefits.
DMET (Drug Metabolizing Enzymes and Transporters) Plus SolutionEnables the cost-effective measurement of ex isting and new metabolic pathway involvement – by providing broad
coverage of relevant pharmacogenetic markers (1,936 genetic variants across 231 relevant genes) in one assay
Provides hig h confidence in results – outstanding assay performance of >99% average sample call rate and >99.8% average
sample reproducibility enables the accurate generation of haplotypes and supports longitudinal and other clinical research studies
Supports the rapid and comprehensive interpretation of g enotyping data – the DMET™ C onsole Software tool translates
genotyping data through to star allele classification and to predicted metabolizer status, allowing the rapid implementation of
genetic understanding in clinical research
Translati ng pharmacogeneti cs into practi ceDMET™ Plus Solution
Applications: Pharmacolog y research – discovery and
application of novel biomarkers resulting from
pharmacogenetic associations
Translational clinical research – longitudinal
clinical research studies designed to generate
comprehensive metabolic profiles
Pre-clinical research and development –
approximately 30% of drug candidates fail during
development due to poor pharmacokinetics
and toxicity, which can be strongly influenced
by genetically determined variation in drug-
metabolizing genes and transporter genes
Industry sponsored clinical research trials –
building databases of known genotypes to show
effects of known metabolic pathways in intermediate
and poor metabolizers and to confirm metabolic
pathway involvement in newly discovered drug
metabolism associations
The DMET Plus Solution: A ssay – Molecular Inversion Probe (MIP) panel
amplifies the precise target DNA of interest
Array – allele-specific oligonucleotide array provides a single color readout on the GeneChip® Scanner 3000 or GeneChip® Scanner 3000Dx v.2, installed in over 2,000 labs globally
Analysis softw are – DMET Console Software provides both the flexibility for user-defined reporting as well as the most comprehensive translation from genotypic data to star allele classification to predicted metabolizer status for the most clinically relevant genes
*During the development of the DMET™ Plus Panel, an average sample pass rate in excess of 95 percent was observed, based on the performance of more than 3,500 samples processed by six sites (three external and three internal). Markers have been evaluated across a minimum of 1,200 individuals including 597 individuals from the extended HapMap population data.
Enabled by a product design that confers high specificity:
Initial multiplexed PCR step to remove pseudogene bias (especially important for C Y P2D6) prior to Molecular
Inversion Probe (MIP) amplification, ensuring the highly specific detection of causative variation
MIP amplification confers multiple levels of enzyme-mediated specificity— polymerization/gap-fill, ligation
and exonuclease digestion; exonuclease digestion reduces background from residual probes and gDNA
prior to amplification
Multiple array capture probes with a unique probe tiling strategy enable highly accurate detection—
even in the presence of known neighboring SNPs
Outstanding data quality
Performance specifications*
Average sample call rate ≥99%
Average sample concordance to reference ≥99.5%
Average sample reproducibility ≥99.8%
Average sample pass rate >95%
G
PCR Primer PCR Primersite 1 site 2
Array Tag sequence
Genomic homology region 1
Genomic homology region 2
1
4
Inverted MIP probe
Probe annealed to genomic DNA
MIP probe before inversion
Cleavage site
1
Anneali
ng
2 Gap fill
3 Ligation
4 Exonuclease digestion and inversion
2 3
G
C
SNP Site
©Affymetrix, Inc. All rights reserved.
Molecular Inversion Probe before, during , and after inversion
* = translated to star allele classification p = translated to predicted phenotype/metabolizer status
DMET™ Plus coverage = 231 genes
M O D IFIER 31
TRANSPORTER 52
PHA S E I 76
PHA S E II 62
TA RGET 10
Comprehensive and relevant genetic content
1,936 SNP, copy number, and indel markers across 231 genes including
many genetic variants that cannot easily be detected by other technologies
(e.g. SNPs and indels with secondary polymorphisms in close proximity,
triallelic markers, and variants from multi-gene families)
100% coverage of PharmaADME “Core ADME Genes” (32 genes) and 95%
coverage of PharmaADME “Core Markers” (185 variants)
Extensive coverage beyond PharmaADME core content to cover common
and functional variants associated with hepatic detoxification for processing
xenobiotics and environmental toxins including: Markers associated with newly described adverse drug events
e.g., C Y P3A4_-392A >G Structural variants in transporter genes – an important pharmaceutical
target e.g., ABCG2_c.421C >A(Q141K) Enrichment for mutations in ADME regulatory genes
e.g., PPARD_c.-101-25241A >G Inclusion of many population specific markers e.g.,
VKORC1_c.-1639G>A
Genes represented by DMET™ Plus Panel
ABCB1 ALDH2 COMT CYP4F3 EPHX2 MAOA RPL13 SLC22A14 TBXAS1 *
ABCB4 ALDH3A1 CROT CYP4F8 FAAH MAOB RXRA SLC25A27 TPMT *p
ABCB7 ALDH3A2 CYP1A1 * CYP4F11 FMO1 MAT1A SERPINA7 SLC28A1 TPSG1
ABCB11 AOX1 CYP1A2 *p CYP4F12 FMO2 * METTL1 SLC5A6 SLC28A2 TYMS
ABCC1 APOA2 CYP1B1 * CYP4Z1 FMO3 NAT1 *p SLC6A6 SLC28A3 UGT1A1 *p
ABCC2 ARNT CYP2A6 *p CYP7A1 FMO4 NAT2 *p SLC7A5 SLC29A1 UGT1A3 *
ABCC3 ARSA CYP2A7 CYP7B1 FMO5 NNMT SLC7A7 SLC29A2 UGT1A4 *
ABCC4 ATP7A CYP2A13* CYP8B1 FMO6 NQO1 SLC7A8 SLCO1A2 UGT1A5
ABCC5 ATP7B CYP2B6 *p CYP11A1 G6PD NR1I2 SLC10A1 SLCO1B1*p UGT1A6 *
ABCC6 CA5P CYP2B7P1 CYP11B1 GSTA1 NR1I3 SLC10A2 SLCO1B3 UGT1A7 *
ABCC8 CBR1 CYP2C8 *p CYP11B2 GSTA2 NR3C1 SLC13A1 SLCO2B1* UGT1A8 *
ABCC9 CBR3 CYP2C9 *p CYP17A1 GSTA3 ORM1 SLC15A1 SLCO3A1 UGT1A9 *
ABCG1 CDA * CYP2C18 CYP19A1* GSTA4 ORM2 SLC15A2* SLCO4A1 UGT1A10*
ABCG2 CES2 CYP2C19*p CYP20A1 GSTA5 PGAP3 SLC16A1 SLCO5A1 UGT2A1
ABP1 CHST1 CYP2D6 *p CYP21A2 GSTM1 *p PNMT SLC19A1 SPG7 UGT2B4
ADH1A CHST2 CYP2E1 *p CYP24A1 GSTM2 PON1 SLC22A1 SPN UGT2B7 *p
ADH1B CHST3 CYP2F1 * CYP26A1 GSTM3 PON2 SLC22A2* SULT1A1* UGT2B11
ADH1C CHST4 CYP2J2 * CYP26C1 GSTM4 PON3 SLC22A3 SULT1A2 UGT2B15*
ADH4 CHST5 CYP2S1 * CYP27A1 GSTM5 POR SLC22A4 SULT1A3 UGT2B17*
ADH5 CHST6 CYP3A4 *p CYP27B1 GSTO1 PPARD SLC22A5 SULT1B1 UGT2B28
ADH6 CHST7 CYP3A5 *p CYP39A1 GSTP1 *p PPARG SLC22A6 SULT1C2 UGT8
ADH7 CHST8 CYP3A7 *p CYP46A1 GSTT1 * PPP1R9A SLC22A7 SULT1C4 VKORC1 *p
AHR CHST9 CYP3A43* CYP51A1 GSTT2 PRSS53 SLC22A8 SULT1E1 XDH
AKAP9 CHST10 CYP4A11 DCK GSTZ1 PTGIS * SLC22A11 SULT2A1
ALB CHST11 CYP4B1 * DPYD * HMGCR QPRT SLC22A12 SULT2B1
ALDH1A1 CHST13 CYP4F2 * EPHX1 HNMT RALBP1 SLC22A13 SULT4A1
DMET™ Console Software offers: Single-sample genotyping – pre-defined marker
boundaries allow samples to be processed in batches of any
size with no impact on reported genotypes
Easy-to-view data – cluster visualization for SNP and
copy number markers
Customized content data reports – user-defined
marker lists for initial genotyping as well as final reports
Translation of genotypes into gene-level diplotypes using
star allele nomenclature and then into a metabolizer status bin
that indicates the relative level of metabolic activity, for example,
the metabolic status bin that describes ultra-rapid metabolizers
(UM), extensive metabolizers (EM), intermediate metabolizers
(IM), and poor metabolizers (PM)
Comprehensive interpretation analysis
DMET™ Plus Workflow –48 hrs to results
Starti ng Noon Day 1
Pre-amplificati on lab
Genomic DNA 1μg (60 ng/μl)
mPCR enrichment
Anneal DNA + MIP probe panel
DMET™ Plus marker summary
Gap-fill, ligation, digestion, & PCR amplification
Hybridization to array
Scan & data analysis
Finished Noon Day 3
Day 1 − PM
Post-amplificati on lab
Day 2Fragmentation
Labeling
Example translation for UGT2B7 gene
Step 3 Ͳ Allele Activity
Step 4 Ͳ Predicted Phenotype
*1a/*1g *2c/*2c *1g/*2c
Stain & wash
Day 3 − A M
Step 2 Ͳ Haplotypes (star allele classification)
Reference Information Translation t orkflow
Step 1 Ͳ Genotypessample 1 sample 2 sample 3
G/G A/A G/A
C/C T/T C/TG/G G/G G/GA/G A/A A/GT/T A/A T/AC/C T/T C/T
UGT2B7 Allele NamescDNA
Position Change *1a *1g *2c *2a *2e *3
Ͳ327G>A Promoter G G A G G GͲ161C>T Promoter C C T C C C211G>T A71S G G G G G T735A>G T245T A G A A A A801T>A P267P T T A T A T802C>T H268Y C C T T T C
1062C>T Y354Y
Allele Activity
? / / /
Extensive Metabolizer
Ultrarapid Metabolizer
Extensive or Ultrarapid
Metabolizer
World-class support
Affymetrix offers an expanding portfolio of customer support and services— from training and instrument maintenance to consulting and compliance—led by our world-class team of multilingual technical experts, field application scientists (FAS), and regional field service engineers (FSE). For more information please visit www.affymetrix.com/service.
A ff ymetrix, Inc. Tel: +1-888-362-2447 A ffymetrix U K Ltd. Tel: +44-(0)1628-552550 A ffymetrix Japan K.K. Tel: +81-(0)3-6430-4020Panomics Soluti ons Tel: +1-877-726-6642 panomics.affymetrix.com USB Products Tel: +1-800-321-9322 www.usb.affymetrix.com
w ww.affymetrix.com Please visit our website for international distributor contact information.“For Research Use Only. Not for use in diagnosti c procedures.”
P/N CL01351 Rev. 2©Affymetrix, Inc. All rights reserved. Affymetrix® , Axiom® , Command Console® , CytoScan® , DMET™ , GeneAtlas® , GeneChip® , GeneChip-compatible™ , GeneTitan® , Genotyping Console™ , myDesign™ , NetAffx® , OncoScan™ , Powered by Affymetrix™ , PrimeView™ , Procarta® , and QuantiGene® are trademarks or registered trademarks of Affymetrix, Inc.All other trademarks are the property of their respective owners.
Products may be covered by one or more of the fol lowing patents: U.S. Patent Nos. 5,445,934; 5,744,305; 5,945,334; 6,140,044; 6,399,365; 6,420,169; 6,551,817; 6,733,977; 7,629,164; 7,790,389 and D430,024 and other U.S. or foreign patents. Products are manufactured and sold under license from OGT under 5,700,637 and 6,054,270.
This industry-recognized instrumentation combined with innovative assays provide a fully integrated system for all your genetic
analysis needs. The DMET™ Plus Solution may be run on either the GeneChip® System 3000 or the G eneChip® System 3000Dx v.2.
The GeneC hip® System (GC S) 3000Dx v.2 is FDA -cleared and includes the G eneC hip® Scanner 3000Dx v.2 with AutoLoaderDx,
GeneChip® Fluidics Station 450Dx v.2, and Workstation with Affymetrix Molecular Diagnostic Software (A MDS). The G eneC hip®
Hybridization Oven 645 is also required. W ith this complete platform, you have every thing you need for hybridiz ing ,
w ashing , staining , and scanning of microarrays.
Flexible, proven, pow erfulThe GeneChip® System 3000 Instrumentation Platform
* “ Research Use Only” (RUO) array requires an array-specific A ssay Software Module (A SM). A custom A SM can be developed for any GeneChip® Array.** FDA -cleared, IVD or C E-marked test developed by a third-party company on the Affymetrix® GC S 3000Dx platform.
Orderin g informationPart number Description
901268 DMET™ Plus Premier PackContains sufficient reagents and arrays for 48 reactions (45 samples and 3 controls)
901495 DMET™ Plus Starter PackContains sufficient reagents and arrays for 8 reactions (7 samples and 1 control)
GeneChip® System 3000Dx v.2 assay menu
Application area RUO* IVD**
3’ IVT expression analysis √ √
Whole-transcript expression analysis √ √
Genotyping/copy number √
Cytogenetic analysis √
Drug metabolism/pharmacogenomics √ √
miRNA gene regulation √
Targeted resequencing √
Custom assays √ √